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UniProtKB - O15550 (KDM6A_HUMAN)

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Protein

Lysine-specific demethylase 6A

Gene

KDM6A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code (PubMed:17851529, PubMed:17713478, PubMed:17761849). Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-27' (PubMed:17851529, PubMed:17713478, PubMed:17761849). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Demethylation of 'Lys-27' of histone H3 is concomitant with methylation of 'Lys-4' of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A (PubMed:17761849). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression (By similarity).By similarity4 Publications

Miscellaneous

Escapes X chromosome inactivation.

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1146Iron1 Publication1
Metal bindingi1148Iron1 Publication1
Metal bindingi1226Iron1 Publication1
Metal bindingi1331Zinc1 Publication1
Metal bindingi1334Zinc1 Publication1
Metal bindingi1358Zinc1 Publication1
Metal bindingi1361Zinc1 Publication1

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3214842 HDMs demethylate histones
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 6A (EC:1.14.11.-4 Publications)
Alternative name(s):
Histone demethylase UTX
Ubiquitously-transcribed TPR protein on the X chromosome
Ubiquitously-transcribed X chromosome tetratricopeptide repeat protein
Gene namesi
Name:KDM6A
Synonyms:UTX
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome X

Organism-specific databases

EuPathDBiHostDB:ENSG00000147050.14
HGNCiHGNC:12637 KDM6A
MIMi300128 gene
neXtProtiNX_O15550

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Kabuki syndrome 2 (KABUK2)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA congenital mental retardation syndrome with additional features, including postnatal dwarfism, a peculiar facies characterized by long palpebral fissures with eversion of the lateral third of the lower eyelids, a broad and depressed nasal tip, large prominent earlobes, a cleft or high-arched palate, scoliosis, short fifth finger, persistence of fingerpads, radiographic abnormalities of the vertebrae, hands, and hip joints, and recurrent otitis media in infancy.
See also OMIM:300867

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1146H → A: Abolishes histone demethylase activity. 3 Publications1

Keywords - Diseasei

Mental retardation

Organism-specific databases

DisGeNETi7403
GeneReviewsiKDM6A
MalaCardsiKDM6A
MIMi300867 phenotype
OpenTargetsiENSG00000147050
Orphaneti2322 Kabuki syndrome
PharmGKBiPA37262

Chemistry databases

ChEMBLiCHEMBL2069164
GuidetoPHARMACOLOGYi2684

Polymorphism and mutation databases

BioMutaiKDM6A

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001064091 – 1401Lysine-specific demethylase 6AAdd BLAST1401

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei519Omega-N-methylarginineBy similarity1
Modified residuei549Omega-N-methylarginineBy similarity1
Modified residuei769PhosphoserineCombined sources1
Modified residuei827PhosphothreonineBy similarity1
Modified residuei829PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiO15550
MaxQBiO15550
PaxDbiO15550
PeptideAtlasiO15550
PRIDEiO15550
ProteomicsDBi48752

PTM databases

iPTMnetiO15550
PhosphoSitePlusiO15550

Expressioni

Gene expression databases

BgeeiENSG00000147050
CleanExiHS_UTX
ExpressionAtlasiO15550 baseline and differential
GenevisibleiO15550 HS

Organism-specific databases

HPAiHPA000568
HPA001165
HPA002111

Interactioni

Subunit structurei

Interacts with TLE1 (By similarity). Component of the MLL2/3 complex (also named ASCOM complex), at least composed of KMT2D/MLL2 or KMT2C/MLL3, ASH2L, RBBP5, WDR5, NCOA6, DPY30, KDM6A (or KDM6B), PAXIP1/PTIP, PAGR1 and alpha- and beta-tubulin (PubMed:17500065, PubMed:17713478). Interacts with SUPT6H. Interacts with SMARCA4 (By similarity).By similarity2 Publications

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGridi113246, 35 interactors
CORUMiO15550
DIPiDIP-46192N
IntActiO15550, 19 interactors
MINTiO15550
STRINGi9606.ENSP00000367203

Chemistry databases

BindingDBiO15550

Structurei

Secondary structure

11401
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi893 – 900Combined sources8
Helixi933 – 935Combined sources3
Beta strandi942 – 944Combined sources3
Helixi948 – 951Combined sources4
Helixi954 – 961Combined sources8
Beta strandi966 – 971Combined sources6
Helixi973 – 977Combined sources5
Helixi981 – 984Combined sources4
Helixi986 – 992Combined sources7
Beta strandi997 – 1004Combined sources8
Beta strandi1016 – 1019Combined sources4
Beta strandi1025 – 1031Combined sources7
Helixi1032 – 1045Combined sources14
Beta strandi1081 – 1089Combined sources9
Turni1093 – 1096Combined sources4
Helixi1097 – 1102Combined sources6
Helixi1103 – 1105Combined sources3
Helixi1108 – 1110Combined sources3
Helixi1118 – 1121Combined sources4
Beta strandi1122 – 1124Combined sources3
Turni1127 – 1129Combined sources3
Beta strandi1133 – 1137Combined sources5
Beta strandi1142 – 1146Combined sources5
Helixi1149 – 1151Combined sources3
Beta strandi1153 – 1162Combined sources10
Beta strandi1164 – 1169Combined sources6
Helixi1171 – 1173Combined sources3
Helixi1174 – 1183Combined sources10
Turni1188 – 1190Combined sources3
Helixi1197 – 1202Combined sources6
Beta strandi1208 – 1212Combined sources5
Beta strandi1217 – 1220Combined sources4
Beta strandi1225 – 1241Combined sources17
Beta strandi1243 – 1245Combined sources3
Helixi1246 – 1262Combined sources17
Helixi1270 – 1280Combined sources11
Helixi1286 – 1312Combined sources27
Beta strandi1317 – 1319Combined sources3
Turni1332 – 1334Combined sources3
Beta strandi1340 – 1346Combined sources7
Beta strandi1351 – 1357Combined sources7
Helixi1359 – 1365Combined sources7
Beta strandi1373 – 1376Combined sources4
Helixi1380 – 1388Combined sources9

3D structure databases

ProteinModelPortaliO15550
SMRiO15550
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati93 – 126TPR 1Add BLAST34
Repeati130 – 163TPR 2Add BLAST34
Repeati170 – 199TPR 3Add BLAST30
Repeati205 – 238TPR 4Add BLAST34
Repeati250 – 283TPR 5Add BLAST34
Repeati284 – 317TPR 6Add BLAST34
Repeati318 – 351TPR 7Add BLAST34
Repeati352 – 385TPR 8Add BLAST34
Domaini1095 – 1258JmjCPROSITE-ProRule annotationAdd BLAST164

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 1095Interaction with SUPT6HBy similarityAdd BLAST1095

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi9 – 17Poly-Ala9

Sequence similaritiesi

Belongs to the UTX family.Curated

Keywords - Domaini

Repeat, TPR repeat

Phylogenomic databases

eggNOGiKOG1124 Eukaryota
KOG1246 Eukaryota
COG0457 LUCA
GeneTreeiENSGT00410000025758
InParanoidiO15550
KOiK11447
PhylomeDBiO15550
TreeFamiTF317405

Family and domain databases

Gene3Di1.25.40.10, 2 hits
InterProiView protein in InterPro
IPR003347 JmjC_dom
IPR029516 KDM6C
IPR013026 TPR-contain_dom
IPR011990 TPR-like_helical_dom_sf
IPR019734 TPR_repeat
PANTHERiPTHR14017:SF9 PTHR14017:SF9, 2 hits
PfamiView protein in Pfam
PF02373 JmjC, 1 hit
PF13181 TPR_8, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00028 TPR, 6 hits
SUPFAMiSSF48452 SSF48452, 2 hits
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS50005 TPR, 7 hits
PS50293 TPR_REGION, 1 hit

Sequencei

Sequence statusi: Complete.

O15550-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKSCGVSLAT AAAAAAAFGD EEKKMAAGKA SGESEEASPS LTAEEREALG 
        60         70         80         90        100
GLDSRLFGFV RFHEDGARTK ALLGKAVRCY ESLILKAEGK VESDFFCQLG 
       110        120        130        140        150
HFNLLLEDYP KALSAYQRYY SLQSDYWKNA AFLYGLGLVY FHYNAFQWAI 
       160        170        180        190        200
KAFQEVLYVD PSFCRAKEIH LRLGLMFKVN TDYESSLKHF QLALVDCNPC 
       210        220        230        240        250
TLSNAEIQFH IAHLYETQRK YHSAKEAYEQ LLQTENLSAQ VKATVLQQLG 
       260        270        280        290        300
WMHHTVDLLG DKATKESYAI QYLQKSLEAD PNSGQSWYFL GRCYSSIGKV 
       310        320        330        340        350
QDAFISYRQS IDKSEASADT WCSIGVLYQQ QNQPMDALQA YICAVQLDHG 
       360        370        380        390        400
HAAAWMDLGT LYESCNQPQD AIKCYLNATR SKSCSNTSAL AARIKYLQAQ 
       410        420        430        440        450
LCNLPQGSLQ NKTKLLPSIE EAWSLPIPAE LTSRQGAMNT AQQNTSDNWS 
       460        470        480        490        500
GGHAVSHPPV QQQAHSWCLT PQKLQHLEQL RANRNNLNPA QKLMLEQLES 
       510        520        530        540        550
QFVLMQQHQM RPTGVAQVRS TGIPNGPTAD SSLPTNSVSG QQPQLALTRV 
       560        570        580        590        600
PSVSQPGVRP ACPGQPLANG PFSAGHVPCS TSRTLGSTDT ILIGNNHITG 
       610        620        630        640        650
SGSNGNVPYL QRNALTLPHN RTNLTSSAEE PWKNQLSNST QGLHKGQSSH 
       660        670        680        690        700
SAGPNGERPL SSTGPSQHLQ AAGSGIQNQN GHPTLPSNSV TQGAALNHLS 
       710        720        730        740        750
SHTATSGGQQ GITLTKESKP SGNILTVPET SRHTGETPNS TASVEGLPNH 
       760        770        780        790        800
VHQMTADAVC SPSHGDSKSP GLLSSDNPQL SALLMGKANN NVGTGTCDKV 
       810        820        830        840        850
NNIHPAVHTK TDNSVASSPS SAISTATPSP KSTEQTTTNS VTSLNSPHSG 
       860        870        880        890        900
LHTINGEGME ESQSPMKTDL LLVNHKPSPQ IIPSMSVSIY PSSAEVLKAC 
       910        920        930        940        950
RNLGKNGLSN SSILLDKCPP PRPPSSPYPP LPKDKLNPPT PSIYLENKRD 
       960        970        980        990       1000
AFFPPLHQFC TNPNNPVTVI RGLAGALKLD LGLFSTKTLV EANNEHMVEV 
      1010       1020       1030       1040       1050
RTQLLQPADE NWDPTGTKKI WHCESNRSHT TIAKYAQYQA SSFQESLREE 
      1060       1070       1080       1090       1100
NEKRSHHKDH SDSESTSSDN SGRRRKGPFK TIKFGTNIDL SDDKKWKLQL 
      1110       1120       1130       1140       1150
HELTKLPAFV RVVSAGNLLS HVGHTILGMN TVQLYMKVPG SRTPGHQENN 
      1160       1170       1180       1190       1200
NFCSVNINIG PGDCEWFVVP EGYWGVLNDF CEKNNLNFLM GSWWPNLEDL 
      1210       1220       1230       1240       1250
YEANVPVYRF IQRPGDLVWI NAGTVHWVQA IGWCNNIAWN VGPLTACQYK 
      1260       1270       1280       1290       1300
LAVERYEWNK LQSVKSIVPM VHLSWNMARN IKVSDPKLFE MIKYCLLRTL 
      1310       1320       1330       1340       1350
KQCQTLREAL IAAGKEIIWH GRTKEEPAHY CSICEVEVFD LLFVTNESNS 
      1360       1370       1380       1390       1400
RKTYIVHCQD CARKTSGNLE NFVVLEQYKM EDLMQVYDQF TLAPPLPSAS 

S
Length:1,401
Mass (Da):154,177
Last modified:September 23, 2008 - v2
Checksum:i9DD7EA6C61E79229
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti173L → V in AAC51839 (PubMed:9381176).Curated1
Sequence conflicti173L → V in AAC51840 (PubMed:9381176).Curated1
Sequence conflicti585L → R in AAC51839 (PubMed:9381176).Curated1
Sequence conflicti585L → R in AAC51840 (PubMed:9381176).Curated1
Sequence conflicti601S → N in AAC51839 (PubMed:9381176).Curated1
Sequence conflicti601S → N in AAC51840 (PubMed:9381176).Curated1
Sequence conflicti629E → K in AAC51839 (PubMed:9381176).Curated1
Sequence conflicti629E → K in AAC51840 (PubMed:9381176).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01449230A → T. Corresponds to variant dbSNP:rs6529EnsemblClinVar.1
Natural variantiVAR_067225270I → V in a patient with chronic myelomonocytic leukemia. 1 Publication1
Natural variantiVAR_014493497Q → H. Corresponds to variant dbSNP:rs6530Ensembl.1
Natural variantiVAR_046527581T → A. Corresponds to variant dbSNP:rs34922269EnsemblClinVar.1
Natural variantiVAR_020313726T → K1 PublicationCorresponds to variant dbSNP:rs2230018EnsemblClinVar.1
Natural variantiVAR_067226834E → D in a patient with chronic myelomonocytic leukemia. 1 Publication1
Natural variantiVAR_067227922R → K in a patient with chronic myelomonocytic leukemia. 1 Publication1
Natural variantiVAR_0358711106L → R in a colorectal cancer sample; somatic mutation. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF000992 mRNA Translation: AAC51839.1
AF000993 mRNA Translation: AAC51840.1
AC136488 Genomic DNA No translation available.
AL133545 Genomic DNA No translation available.
AL138744 Genomic DNA No translation available.
CH471141 Genomic DNA Translation: EAW59368.1
BC093868 mRNA Translation: AAH93868.1
BC113381 mRNA Translation: AAI13382.1
CCDSiCCDS14265.1
PIRiT02255
RefSeqiNP_066963.2, NM_021140.3
UniGeneiHs.522616

Genome annotation databases

EnsembliENST00000377967; ENSP00000367203; ENSG00000147050
GeneIDi7403
KEGGihsa:7403
UCSCiuc004dge.5 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiKDM6A_HUMAN
AccessioniPrimary (citable) accession number: O15550
Secondary accession number(s): Q52LL9, Q5JVQ7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: September 23, 2008
Last modified: July 18, 2018
This is version 180 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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